TY - JOUR
T1 - Precise dissection of an escherichia coli o157:H7 outbreak by single nucleotide polymorphism analysis
AU - Turabelidze, George
AU - Lawrence, Steven J.
AU - Gao, Hongyu
AU - Sodergren, Erica
AU - Weinstock, George M.
AU - Abubucker, Sahar
AU - Wylie, Todd
AU - Mitreva, Makedonka
AU - Shaikh, Nurmohammad
AU - Gautom, Romesh
AU - Tarr, Phillip I.
PY - 2013/12
Y1 - 2013/12
N2 - The current pathogen-typing methods have suboptimal sensitivities and specificities. DNA sequencing offers an opportunity to type pathogens with greater degrees of discrimination using single nucleotide polymorphisms (SNPs) than with pulsed-field gel electrophoresis (PFGE) and other methodologies. In a recent cluster of Escherichia coli O157:H7 infections attributed to salad bar exposures and romaine lettuce, a subset of cases denied exposure to either source, although PFGE and multiple-locus variable-number tandem-repeat analysis (MLVA) suggested that all isolates had the same recent progenitor. Interrogation of a preselected set of 3,442,673 nucleotides in backbone open reading frames (ORFs) identified only 1 or 2 single nucleotide differences in 3 of 12 isolates from the cases who denied exposure. The backbone DNAs of 9 of 9 and 3 of 3 cases who reported or were unsure about exposure, respectively, were isogenic. Backbone ORF SNP set sequencing offers pathogen differentiation capabilities that exceed those of PFGE and MLVA.
AB - The current pathogen-typing methods have suboptimal sensitivities and specificities. DNA sequencing offers an opportunity to type pathogens with greater degrees of discrimination using single nucleotide polymorphisms (SNPs) than with pulsed-field gel electrophoresis (PFGE) and other methodologies. In a recent cluster of Escherichia coli O157:H7 infections attributed to salad bar exposures and romaine lettuce, a subset of cases denied exposure to either source, although PFGE and multiple-locus variable-number tandem-repeat analysis (MLVA) suggested that all isolates had the same recent progenitor. Interrogation of a preselected set of 3,442,673 nucleotides in backbone open reading frames (ORFs) identified only 1 or 2 single nucleotide differences in 3 of 12 isolates from the cases who denied exposure. The backbone DNAs of 9 of 9 and 3 of 3 cases who reported or were unsure about exposure, respectively, were isogenic. Backbone ORF SNP set sequencing offers pathogen differentiation capabilities that exceed those of PFGE and MLVA.
UR - http://www.scopus.com/inward/record.url?scp=84889793277&partnerID=8YFLogxK
U2 - 10.1128/JCM.01930-13
DO - 10.1128/JCM.01930-13
M3 - Article
C2 - 24048526
AN - SCOPUS:84889793277
SN - 0095-1137
VL - 51
SP - 3950
EP - 3954
JO - Journal of clinical microbiology
JF - Journal of clinical microbiology
IS - 12
ER -